PDB Short entry for 10MH HEADER TRANSFERASE/DNA 10-AUG-98 10MH TITLE TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND TITLE 2 HEMIMETHYLATED DNA CONTAINING 5,6-DIHYDRO-5-AZACYTOSINE AT THE TARGET COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*GP*TP*CP*AP*GP*5NCP*GP*CP*AP*TP*GP*G)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PROTEIN (CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI); COMPND 11 CHAIN: A; COMPND 12 SYNONYM: MODIFICATION METHYLASE HHAI, M.HHAI; COMPND 13 EC: 2.1.1.73; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HAEMOPHILUS HAEMOLYTICUS; SOURCE 7 ORGANISM_TAXID: 726; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE, METHYLTRANSFERASE, RESTRICTION SYSTEM, COMPLEX KEYWDS 2 (METHYLTRANSFERASE- DNA), TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.SHEIKHNEJAD,A.BRANK,J.K.CHRISTMAN,A.GODDARD,E.ALVAREZ,H.FORD AUTHOR 2 JUNIOR,V.E.MARQUEZ,C.J.MARASCO,J.R.SUFRIN,M.O'GARA,X.CHENG REVDAT 6 09-AUG-23 10MH 1 REMARK LINK REVDAT 5 24-FEB-09 10MH 1 VERSN REVDAT 4 01-APR-03 10MH 1 JRNL REVDAT 3 20-JUN-00 10MH 1 REMARK CRYST1 REVDAT 2 22-DEC-99 10MH 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 09-FEB-99 10MH 0 JRNL AUTH G.SHEIKHNEJAD,A.BRANK,J.K.CHRISTMAN,A.GODDARD,E.ALVAREZ, JRNL AUTH 2 H.FORD JR.,V.E.MARQUEZ,C.J.MARASCO,J.R.SUFRIN,M.O'GARA, JRNL AUTH 3 X.CHENG JRNL TITL MECHANISM OF INHIBITION OF DNA (CYTOSINE JRNL TITL 2 C5)-METHYLTRANSFERASES BY OLIGODEOXYRIBONUCLEOTIDES JRNL TITL 3 CONTAINING 5,6-DIHYDRO-5-AZACYTOSINE. JRNL REF J.MOL.BIOL. V. 285 2021 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 9925782 JRNL DOI 10.1006/JMBI.1998.2426 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 76.6 REMARK 3 NUMBER OF REFLECTIONS : 15965 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 51.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1311 REMARK 3 BIN R VALUE (WORKING SET) : 0.3200 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2606 REMARK 3 NUCLEIC ACID ATOMS : 493 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.600 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 10MH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008103. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-96 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.15 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15976 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 77.2 REMARK 200 DATA REDUNDANCY : 3.230 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.890 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 5MHT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (W/V) PEG 8000 50 MM CALCIUM REMARK 280 ACETATE 50 MM SODIUM CACODYLATE PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 49.93000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 28.82710 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 108.40000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 49.93000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 28.82710 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 108.40000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 49.93000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 28.82710 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 108.40000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 49.93000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 28.82710 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 108.40000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 49.93000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 28.82710 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 108.40000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 49.93000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 28.82710 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 108.40000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 57.65420 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 216.80000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 57.65420 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 216.80000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 57.65420 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 216.80000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 57.65420 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 216.80000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 57.65420 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 216.80000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 57.65420 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 216.80000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 HIS A 275 O HOH A 470 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC B 402 P DC B 402 O5' 0.072 REMARK 500 DC B 402 N3 DC B 402 C4 0.058 REMARK 500 DC B 403 C2 DC B 403 N3 0.070 REMARK 500 DA B 404 C5 DA B 404 N7 -0.049 REMARK 500 DT B 405 C5' DT B 405 C4' 0.063 REMARK 500 DT B 405 C5 DT B 405 C6 0.060 REMARK 500 DG B 406 C5' DG B 406 C4' 0.083 REMARK 500 DG B 406 O3' DG B 406 C3' 0.088 REMARK 500 DG B 406 N9 DG B 406 C4 0.097 REMARK 500 DG B 408 C5' DG B 408 C4' 0.102 REMARK 500 DG B 408 C5 DG B 408 N7 0.039 REMARK 500 DC B 409 C5' DC B 409 C4' 0.067 REMARK 500 DT B 410 C5' DT B 410 C4' 0.051 REMARK 500 DT B 410 O3' DG B 411 P 0.085 REMARK 500 DG B 411 N3 DG B 411 C4 -0.051 REMARK 500 DA B 412 N3 DA B 412 C4 0.039 REMARK 500 DA B 412 C5 DA B 412 N7 0.056 REMARK 500 DA B 412 C8 DA B 412 N9 0.070 REMARK 500 DA B 412 N9 DA B 412 C4 0.061 REMARK 500 DA B 412 O3' DC B 413 P 0.201 REMARK 500 DC B 413 P DC B 413 O5' 0.072 REMARK 500 DC B 413 N1 DC B 413 C6 0.037 REMARK 500 DG C 422 P DG C 422 O5' 0.131 REMARK 500 DG C 422 C5' DG C 422 C4' 0.086 REMARK 500 DG C 422 C2' DG C 422 C1' -0.222 REMARK 500 DG C 422 O4' DG C 422 C1' 0.254 REMARK 500 DT C 423 O3' DT C 423 C3' -0.041 REMARK 500 DT C 423 C6 DT C 423 N1 -0.050 REMARK 500 DC C 424 O3' DA C 425 P -0.074 REMARK 500 DA C 425 P DA C 425 O5' 0.066 REMARK 500 DA C 425 O3' DG C 426 P -0.081 REMARK 500 DG C 426 C5' DG C 426 C4' 0.063 REMARK 500 DG C 428 P DG C 428 O5' -0.092 REMARK 500 DG C 428 C5' DG C 428 C4' 0.082 REMARK 500 DC C 429 P DC C 429 O5' 0.083 REMARK 500 DC C 429 C5' DC C 429 C4' 0.135 REMARK 500 DC C 429 O3' DA C 430 P 0.085 REMARK 500 DA C 430 C5' DA C 430 C4' 0.066 REMARK 500 DA C 430 O3' DT C 431 P 0.072 REMARK 500 DT C 431 C5' DT C 431 C4' 0.074 REMARK 500 DT C 431 C1' DT C 431 N1 0.121 REMARK 500 DT C 431 N1 DT C 431 C2 0.051 REMARK 500 DG C 433 C2 DG C 433 N3 0.055 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC B 402 O4' - C4' - C3' ANGL. DEV. = -9.4 DEGREES REMARK 500 DC B 402 C6 - N1 - C2 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 402 N1 - C2 - N3 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC B 402 N3 - C4 - N4 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC B 402 C5 - C4 - N4 ANGL. DEV. = -5.5 DEGREES REMARK 500 DC B 403 O4' - C4' - C3' ANGL. DEV. = -10.0 DEGREES REMARK 500 DC B 403 O4' - C1' - C2' ANGL. DEV. = -11.7 DEGREES REMARK 500 DC B 403 N3 - C4 - N4 ANGL. DEV. = 6.3 DEGREES REMARK 500 DC B 403 C5 - C4 - N4 ANGL. DEV. = -5.7 DEGREES REMARK 500 DC B 403 C3' - O3' - P ANGL. DEV. = 10.8 DEGREES REMARK 500 DA B 404 O5' - P - OP2 ANGL. DEV. = -9.3 DEGREES REMARK 500 DA B 404 O4' - C4' - C3' ANGL. DEV. = -4.5 DEGREES REMARK 500 DA B 404 O4' - C1' - C2' ANGL. DEV. = -12.6 DEGREES REMARK 500 DA B 404 N9 - C1' - C2' ANGL. DEV. = 9.4 DEGREES REMARK 500 DA B 404 O4' - C1' - N9 ANGL. DEV. = -9.3 DEGREES REMARK 500 DA B 404 N1 - C2 - N3 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA B 404 C2 - N3 - C4 ANGL. DEV. = -5.4 DEGREES REMARK 500 DA B 404 C4 - C5 - C6 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA B 404 C5 - C6 - N1 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA B 404 N1 - C6 - N6 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 404 C3' - O3' - P ANGL. DEV. = 13.1 DEGREES REMARK 500 DT B 405 O3' - P - O5' ANGL. DEV. = -14.3 DEGREES REMARK 500 DT B 405 O5' - P - OP2 ANGL. DEV. = 7.7 DEGREES REMARK 500 DT B 405 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 DT B 405 O4' - C1' - C2' ANGL. DEV. = -8.2 DEGREES REMARK 500 DT B 405 N1 - C2 - N3 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT B 405 N3 - C4 - C5 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT B 405 C4 - C5 - C6 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT B 405 C4 - C5 - C7 ANGL. DEV. = -6.7 DEGREES REMARK 500 DT B 405 C3' - O3' - P ANGL. DEV. = 10.3 DEGREES REMARK 500 DG B 406 O3' - P - O5' ANGL. DEV. = -13.0 DEGREES REMARK 500 DG B 406 P - O5' - C5' ANGL. DEV. = 10.0 DEGREES REMARK 500 DG B 406 C4' - C3' - C2' ANGL. DEV. = -8.6 DEGREES REMARK 500 DG B 406 O4' - C1' - C2' ANGL. DEV. = -16.2 DEGREES REMARK 500 DG B 406 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DG B 406 N3 - C4 - C5 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG B 406 N3 - C4 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG B 406 C6 - C5 - N7 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG B 408 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 DC B 409 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 DC B 409 O4' - C1' - C2' ANGL. DEV. = -15.3 DEGREES REMARK 500 DC B 409 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC B 409 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC B 409 N3 - C4 - C5 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC B 409 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 DT B 410 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 DT B 410 O4' - C1' - C2' ANGL. DEV. = -7.7 DEGREES REMARK 500 DT B 410 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT B 410 C6 - N1 - C2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT B 410 C4 - C5 - C6 ANGL. DEV. = 5.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 105 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 37 132.92 178.54 REMARK 500 GLU A 40 134.94 -171.80 REMARK 500 GLU A 58 -179.51 -68.30 REMARK 500 ASP A 60 108.87 11.56 REMARK 500 PHE A 84 -25.54 -144.20 REMARK 500 HIS A 127 138.47 -39.43 REMARK 500 ASP A 144 49.17 78.89 REMARK 500 ASN A 176 18.89 56.42 REMARK 500 PHE A 259 43.42 -107.62 REMARK 500 ALA A 260 135.98 -38.60 REMARK 500 LYS A 261 -36.54 68.29 REMARK 500 ASN A 268 42.93 39.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC B 409 0.06 SIDE CHAIN REMARK 500 DG C 428 0.05 SIDE CHAIN REMARK 500 DG C 432 0.07 SIDE CHAIN REMARK 500 DG C 433 0.05 SIDE CHAIN REMARK 500 TYR A 265 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 328 DBREF 10MH A 1 327 UNP P05102 MTH1_HAEHA 1 327 DBREF 10MH B 402 413 PDB 10MH 10MH 402 413 DBREF 10MH C 422 433 PDB 10MH 10MH 422 433 SEQRES 1 B 12 DC DC DA DT DG 5CM DG DC DT DG DA DC SEQRES 1 C 12 DG DT DC DA DG 5NC DG DC DA DT DG DG SEQRES 1 A 327 MET ILE GLU ILE LYS ASP LYS GLN LEU THR GLY LEU ARG SEQRES 2 A 327 PHE ILE ASP LEU PHE ALA GLY LEU GLY GLY PHE ARG LEU SEQRES 3 A 327 ALA LEU GLU SER CYS GLY ALA GLU CYS VAL TYR SER ASN SEQRES 4 A 327 GLU TRP ASP LYS TYR ALA GLN GLU VAL TYR GLU MET ASN SEQRES 5 A 327 PHE GLY GLU LYS PRO GLU GLY ASP ILE THR GLN VAL ASN SEQRES 6 A 327 GLU LYS THR ILE PRO ASP HIS ASP ILE LEU CYS ALA GLY SEQRES 7 A 327 PHE PRO CYS GLN ALA PHE SER ILE SER GLY LYS GLN LYS SEQRES 8 A 327 GLY PHE GLU ASP SER ARG GLY THR LEU PHE PHE ASP ILE SEQRES 9 A 327 ALA ARG ILE VAL ARG GLU LYS LYS PRO LYS VAL VAL PHE SEQRES 10 A 327 MET GLU ASN VAL LYS ASN PHE ALA SER HIS ASP ASN GLY SEQRES 11 A 327 ASN THR LEU GLU VAL VAL LYS ASN THR MET ASN GLU LEU SEQRES 12 A 327 ASP TYR SER PHE HIS ALA LYS VAL LEU ASN ALA LEU ASP SEQRES 13 A 327 TYR GLY ILE PRO GLN LYS ARG GLU ARG ILE TYR MET ILE SEQRES 14 A 327 CYS PHE ARG ASN ASP LEU ASN ILE GLN ASN PHE GLN PHE SEQRES 15 A 327 PRO LYS PRO PHE GLU LEU ASN THR PHE VAL LYS ASP LEU SEQRES 16 A 327 LEU LEU PRO ASP SER GLU VAL GLU HIS LEU VAL ILE ASP SEQRES 17 A 327 ARG LYS ASP LEU VAL MET THR ASN GLN GLU ILE GLU GLN SEQRES 18 A 327 THR THR PRO LYS THR VAL ARG LEU GLY ILE VAL GLY LYS SEQRES 19 A 327 GLY GLY GLN GLY GLU ARG ILE TYR SER THR ARG GLY ILE SEQRES 20 A 327 ALA ILE THR LEU SER ALA TYR GLY GLY GLY ILE PHE ALA SEQRES 21 A 327 LYS THR GLY GLY TYR LEU VAL ASN GLY LYS THR ARG LYS SEQRES 22 A 327 LEU HIS PRO ARG GLU CYS ALA ARG VAL MET GLY TYR PRO SEQRES 23 A 327 ASP SER TYR LYS VAL HIS PRO SER THR SER GLN ALA TYR SEQRES 24 A 327 LYS GLN PHE GLY ASN SER VAL VAL ILE ASN VAL LEU GLN SEQRES 25 A 327 TYR ILE ALA TYR ASN ILE GLY SER SER LEU ASN PHE LYS SEQRES 26 A 327 PRO TYR MODRES 10MH 5CM B 407 DC MODRES 10MH 5NC C 427 DC 5-AZA-CYTIDINE-5'MONOPHOSPHATE HET 5CM B 407 20 HET 5NC C 427 19 HET SAH A 328 26 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM 5NC 5-AZA-CYTIDINE-5'MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 1 5CM C10 H16 N3 O7 P FORMUL 2 5NC C8 H13 N4 O7 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 HOH *129(H2 O) HELIX 1 1 GLY A 23 GLU A 29 1 7 HELIX 2 2 LYS A 43 PHE A 53 1 11 HELIX 3 3 ILE A 61 GLN A 63 5 3 HELIX 4 4 GLY A 92 GLU A 94 5 3 HELIX 5 5 LEU A 100 LYS A 111 5 12 HELIX 6 6 LYS A 122 ALA A 125 5 4 HELIX 7 7 HIS A 127 GLU A 142 5 16 HELIX 8 8 ALA A 154 ASP A 156 5 3 HELIX 9 9 ASN A 173 LEU A 175 5 3 HELIX 10 10 VAL A 192 ASP A 194 5 3 HELIX 11 11 ASP A 199 GLU A 201 5 3 HELIX 12 12 GLU A 203 LEU A 205 5 3 HELIX 13 13 PRO A 276 MET A 283 1 8 HELIX 14 14 THR A 295 ASN A 304 1 10 HELIX 15 15 ILE A 308 LEU A 322 1 15 SHEET 1 A 5 PHE A 14 LEU A 17 0 SHEET 2 A 5 ILE A 74 GLY A 78 1 N ILE A 74 O ILE A 15 SHEET 3 A 5 VAL A 115 VAL A 121 1 N VAL A 115 O LEU A 75 SHEET 4 A 5 GLU A 164 PHE A 171 -1 N CYS A 170 O VAL A 116 SHEET 5 A 5 HIS A 148 ASN A 153 -1 N LEU A 152 O ARG A 165 SHEET 1 B 4 LYS A 270 ARG A 272 0 SHEET 2 B 4 GLY A 264 VAL A 267 -1 N VAL A 267 O LYS A 270 SHEET 3 B 4 ARG A 240 SER A 243 1 N TYR A 242 O GLY A 264 SHEET 4 B 4 ARG A 228 ILE A 231 -1 N GLY A 230 O ILE A 241 LINK O3' DG B 406 P 5CM B 407 1555 1555 1.66 LINK O3' 5CM B 407 P DG B 408 1555 1555 1.63 LINK O3' DG C 426 P 5NC C 427 1555 1555 1.64 LINK O3' 5NC C 427 P DG C 428 1555 1555 1.62 SITE 1 AC1 18 PHE A 18 ALA A 19 GLY A 20 LEU A 21 SITE 2 AC1 18 GLY A 23 ASN A 39 GLU A 40 TRP A 41 SITE 3 AC1 18 ASP A 60 ILE A 61 GLY A 78 ASN A 304 SITE 4 AC1 18 SER A 305 VAL A 306 HOH A 338 HOH A 340 SITE 5 AC1 18 HOH A 384 HOH A 451 CRYST1 99.860 99.860 325.200 90.00 90.00 120.00 H 3 2 18 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010014 0.005781 0.000000 0.00000 SCALE2 0.000000 0.011563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003075 0.00000